The risk of breast cancer (“BC”) varies between women, and genetic susceptibility plays an important role in the etiology of the disease; highly-penetrant alleles are estimated to account for up to 10% of all BC [1]. Two major breast cancer susceptibility genes, BRCA1 and BRCA2, were identified in the 1990s; they are responsible for ˜15% to 20% of inherited BC [1-3]. Since then, other genes, such as ATM, CHEK2, NBN, PALB2, PTEN, and TP53, have been identified [4-9]. Together, all known breast cancer susceptibility genes are estimated to account for one-half of hereditary BC cases [1]. The genes responsible for the remaining ˜50% are yet to be determined. Accordingly, there remains a need to identify further prognostic and diagnostic markers for breast cancer and to develop methods for determining a subject's susceptibility to breast cancer.
In genetically homogenous populations, seemingly unrelated affected individuals may, in fact, be distantly related and may share a mutant susceptibility allele inherited from a common ancestor. In these situations, by using highly parallel DNA sequencing methods, it is possible to look for associations with specific (causative) alleles, rather than to use linked genetic markers or to identify and sum multiple genetic variants at a single gene locus. Currently, exome sequencing facilitates the determination of all variants in an individual's genome coding regions through comparison to the reference sequence. Exome sequencing was first used successfully in 2009 to identify the gene mutation underlying Miller syndrome [17] and since then it has been employed to detect many other Mendelian rare genetic disorders. However, it has been less successful in identifying genes underlying complex disorders, like cancer.